The visitors were 11 overs short of their target as England won the match by eight wickets to sweep the series 3-0, the ICC said in a statement.
The deduction leaves Pakistan rooted to the bottom of the standings with five points in nine matches.
Australia, who have won eight of their 10 tests in the current cycle, lead the table with defending champions South Africa second.
The top two teams meet in the final at the Oval in London in June 2027.
Pakistan's next tests are against Sri Lanka in a two-match home series in November.